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Reina C, Šabanović B, Lazzari C, Gregorc V, Heeschen C. Unlocking the future of cancer diagnosis - promises and challenges of ctDNA-based liquid biopsies in non-small cell lung cancer. Transl Res 2024; 272:41-53. [PMID: 38838851 DOI: 10.1016/j.trsl.2024.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/29/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024]
Abstract
The advent of liquid biopsies has brought significant changes to the diagnosis and monitoring of non-small cell lung cancer (NSCLC), presenting both promise and challenges. Molecularly targeted drugs, capable of enhancing survival rates, are now available to around a quarter of NSCLC patients. However, to ensure their effectiveness, precision diagnosis is essential. Circulating tumor DNA (ctDNA) analysis as the most advanced liquid biopsy modality to date offers a non-invasive method for tracking genomic changes in NSCLC. The potential of ctDNA is particularly rooted in its ability to furnish comprehensive (epi-)genetic insights into the tumor, thereby aiding personalized treatment strategies. One of the key advantages of ctDNA-based liquid biopsies in NSCLC is their ability to capture tumor heterogeneity. This capability ensures a more precise depiction of the tumor's (epi-)genomic landscape compared to conventional tissue biopsies. Consequently, it facilitates the identification of (epi-)genetic alterations, enabling informed treatment decisions, disease progression monitoring, and early detection of resistance-causing mutations for timely therapeutic interventions. Here we review the current state-of-the-art in ctDNA-based liquid biopsy technologies for NSCLC, exploring their potential to revolutionize clinical practice. Key advancements in ctDNA detection methods, including PCR-based assays, next-generation sequencing (NGS), and digital PCR (dPCR), are discussed, along with their respective strengths and limitations. Additionally, the clinical utility of ctDNA analysis in guiding treatment decisions, monitoring treatment response, detecting minimal residual disease, and identifying emerging resistance mechanisms is examined. Liquid biopsy analysis bears the potential of transforming NSCLC management by enabling non-invasive monitoring of Minimal Residual Disease and providing early indicators for response to targeted treatments including immunotherapy. Furthermore, considerations regarding sample collection, processing, and data interpretation are highlighted as crucial factors influencing the reliability and reproducibility of ctDNA-based assays. Addressing these challenges will be essential for the widespread adoption of ctDNA-based liquid biopsies in routine clinical practice, ultimately paving the way toward personalized medicine and improved outcomes for patients with NSCLC.
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Affiliation(s)
- Chiara Reina
- Pancreatic Cancer Heterogeneity, Candiolo Cancer Institute FPO-IRCCS, Candiolo, Turin, Italy
| | - Berina Šabanović
- Pancreatic Cancer Heterogeneity, Candiolo Cancer Institute FPO-IRCCS, Candiolo, Turin, Italy
| | - Chiara Lazzari
- Department of Medical Oncology, Cancer Institute FPO-IRCCS, Candiolo, Turin, Italy
| | - Vanesa Gregorc
- Department of Medical Oncology, Cancer Institute FPO-IRCCS, Candiolo, Turin, Italy
| | - Christopher Heeschen
- Pancreatic Cancer Heterogeneity, Candiolo Cancer Institute FPO-IRCCS, Candiolo, Turin, Italy;.
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Wang Y, Liu H, Zhang M, Xu J, Zheng L, Liu P, Chen J, Liu H, Chen C. Epigenetic reprogramming in gastrointestinal cancer: biology and translational perspectives. MedComm (Beijing) 2024; 5:e670. [PMID: 39184862 PMCID: PMC11344282 DOI: 10.1002/mco2.670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 08/27/2024] Open
Abstract
Gastrointestinal tumors, the second leading cause of human mortality, are characterized by their association with inflammation. Currently, progress in the early diagnosis and effective treatment of gastrointestinal tumors is limited. Recent whole-genome analyses have underscored their profound heterogeneity and extensive genetic and epigenetic reprogramming. Epigenetic reprogramming pertains to dynamic and hereditable alterations in epigenetic patterns, devoid of concurrent modifications in the underlying DNA sequence. Common epigenetic modifications encompass DNA methylation, histone modifications, noncoding RNA, RNA modifications, and chromatin remodeling. These modifications possess the potential to invoke or suppress a multitude of genes associated with cancer, thereby governing the establishment of chromatin configurations characterized by diverse levels of accessibility. This intricate interplay assumes a pivotal and indispensable role in governing the commencement and advancement of gastrointestinal cancer. This article focuses on the impact of epigenetic reprogramming in the initiation and progression of gastric cancer, esophageal cancer, and colorectal cancer, as well as other uncommon gastrointestinal tumors. We elucidate the epigenetic landscape of gastrointestinal tumors, encompassing DNA methylation, histone modifications, chromatin remodeling, and their interrelationships. Besides, this review summarizes the potential diagnostic, therapeutic, and prognostic targets in epigenetic reprogramming, with the aim of assisting clinical treatment strategies.
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Affiliation(s)
- Yingjie Wang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Hongyu Liu
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Mengsha Zhang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Jing Xu
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Liuxian Zheng
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Pengpeng Liu
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Jingyao Chen
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Hongyu Liu
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Chong Chen
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina
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McMurry HS, Rivero JD, Chen EY, Kardosh A, Lopez CD, Pegna GJ. Gastroenteropancreatic neuroendocrine tumors: Epigenetic landscape and clinical implications. Curr Probl Cancer 2024; 52:101131. [PMID: 39173542 DOI: 10.1016/j.currproblcancer.2024.101131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/22/2024] [Indexed: 08/24/2024]
Abstract
Neuroendocrine tumors (NETs) are a rare, heterogenous group of neoplasms arising from cells of the neuroendocrine system. Amongst solid tumor malignancies, NETs are notable for overall genetic stability and recent data supports the notion that epigenetic changes may drive NET pathogenesis. In this review, major epigenetic mechanisms of NET pathogenesis are reviewed, including changes in DNA methylation, histone modification, chromatin remodeling, and microRNA. Prognostic implications of the above are discussed, as well as the expanding diagnostic utility of epigenetic markers in NETs. Lastly, preclinical and clinical evaluations of epigenetically targeted therapies in NETs and are reviewed, with a focus on future directions in therapeutic advancement.
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Affiliation(s)
- Hannah S McMurry
- Department of Medicine, Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR, United States
| | - Jaydira Del Rivero
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emerson Y Chen
- Department of Medicine, Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR, United States
| | - Adel Kardosh
- Department of Medicine, Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR, United States
| | - Charles D Lopez
- Department of Medicine, Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR, United States
| | - Guillaume J Pegna
- Department of Medicine, Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR, United States.
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Foffano L, Vida R, Piacentini A, Molteni E, Cucciniello L, Da Ros L, Silvia B, Cereser L, Roncato R, Gerratana L, Puglisi F. Is ctDNA ready to outpace imaging in monitoring early and advanced breast cancer? Expert Rev Anticancer Ther 2024; 24:679-691. [PMID: 38855809 DOI: 10.1080/14737140.2024.2362173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
INTRODUCTION Circulating tumor DNA (ctDNA) and radiological imaging are increasingly recognized as crucial elements in breast cancer management. While radiology remains the cornerstone for screening and monitoring, ctDNA holds distinctive advantages in anticipating diagnosis, recurrence, or progression, providing concurrent biological insights complementary to imaging results. AREAS COVERED This review delves into the current evidence on the synergistic relationship between ctDNA and imaging in breast cancer. It presents data on the clinical validity and utility of ctDNA in both early and advanced settings, providing insights into emerging liquid biopsy techniques like epigenetics and fragmentomics. Simultaneously, it explores the present and future landscape of imaging methodologies, particularly focusing on radiomics. EXPERT OPINION Numerous are the current technical, strategic, and economic challenges preventing the clinical integration of ctDNA analysis in the breast cancer monitoring. Understanding these complexities and devising targeted strategies is pivotal to effectively embedding this methodology into personalized patient care.
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Affiliation(s)
- Lorenzo Foffano
- Department of Medicine, University of Udine, Udine, Italy
- Department of Medical Oncology, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
| | - Riccardo Vida
- Department of Medicine, University of Udine, Udine, Italy
- Department of Medical Oncology, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
| | | | - Elisabetta Molteni
- Department of Medicine, University of Udine, Udine, Italy
- Weill Cornell Medicine, Department of Medicine, Division of Hematology-Oncology, New York, NY, USA
| | - Linda Cucciniello
- Department of Medicine, University of Udine, Udine, Italy
- Department of Medical Oncology, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
| | - Lucia Da Ros
- Department of Medical Oncology, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
| | - Buriolla Silvia
- Department of Oncology, Santa Maria della Misericordia University Hospital, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Lorenzo Cereser
- Department of Medicine, University of Udine, Udine, Italy
- Azienda Sanitaria-Universitaria Friuli Centrale (ASUFC), University Hospital S. Maria della Misericordia, Udine, Italy
| | | | - Lorenzo Gerratana
- Department of Medicine, University of Udine, Udine, Italy
- Department of Medical Oncology, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
| | - Fabio Puglisi
- Department of Medicine, University of Udine, Udine, Italy
- Department of Medical Oncology, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
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Bakker A, Ixkes AE, Venugopal H, Ries MG, Lak NSM, de Vos FYFL, van Vuurden DG, Snijders TJ. Focused Ultrasound-Enhanced Liquid Biopsy: A Promising Diagnostic Tool for Brain Tumor Patients. Cancers (Basel) 2024; 16:1576. [PMID: 38672658 PMCID: PMC11049441 DOI: 10.3390/cancers16081576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
The performance of minimally invasive molecular diagnostic tools in brain tumors, such as liquid biopsy, has so far been limited by the blood-brain barrier (BBB). The BBB hinders the release of brain tumor biomarkers into the bloodstream. The use of focused ultrasound in conjunction with microbubbles has been shown to temporarily open the BBB (FUS-BBBO). This may enhance blood-based tumor biomarker levels. This systematic review provides an overview of the data regarding FUS-BBBO-enhanced liquid biopsy for primary brain tumors. A systematic search was conducted in PubMed and Embase databases with key terms "brain tumors", "liquid biopsy", "FUS" and their synonyms, in accordance with PRISMA statement guidelines. Five preclinical and two clinical studies were included. Preclinical studies utilized mouse, rat and porcine glioma models. Biomarker levels were found to be higher in sonicated groups compared to control groups. Both stable and inertial microbubble cavitation increased biomarker levels, whereas only inertial cavitation induced microhemorrhages. In clinical studies involving 14 patients with high-grade brain tumors, biomarker levels were increased after FUS-BBBO with stable cavitation. In conclusion, FUS-BBBO-enhanced liquid biopsy using stable cavitation shows diagnostic potential for primary brain tumors. Further research is imperative before integrating FUS-BBBO for liquid biopsy enhancement into clinical practice.
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Affiliation(s)
- Akke Bakker
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands
- Department of Neurology & Neurosurgery, UMC Utrecht Brain Center, UMC Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Anna E. Ixkes
- Biomedical Sciences, Utrecht University, Heidelberglaan 8, 3584 CS Utrecht, The Netherlands
| | - Hema Venugopal
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands
- Department of Neurology & Neurosurgery, UMC Utrecht Brain Center, UMC Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Mario G. Ries
- Imaging Division, UMC Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Nathalie S. M. Lak
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands
| | - Filip Y. F. L. de Vos
- Department of Medical Oncology, UMC Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Dannis G. van Vuurden
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands
| | - Tom J. Snijders
- Department of Neurology & Neurosurgery, UMC Utrecht Brain Center, UMC Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
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Swiatlowska P, Iskratsch T. Cardiovascular Mechano-Epigenetics: Force-Dependent Regulation of Histone Modifications and Gene Regulation. Cardiovasc Drugs Ther 2024; 38:215-222. [PMID: 36653625 PMCID: PMC10959834 DOI: 10.1007/s10557-022-07422-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/28/2022] [Indexed: 01/19/2023]
Abstract
The local mechanical microenvironment impacts on the cell behavior. In the cardiovascular system, cells in both the heart and the vessels are exposed to continuous blood flow, blood pressure, stretching forces, and changing extracellular matrix stiffness. The force-induced signals travel all the way to the nucleus regulating epigenetic changes such as chromatin dynamics and gene expression. Mechanical cues are needed at the very early stage for a faultless embryological development, while later in life, aberrant mechanical signaling can lead to a range of pathologies, including diverse cardiovascular diseases. Hence, an investigation of force-generated epigenetic alteration at different time scales is needed to understand fully the phenotypic changes in disease onset and progression. That being so, cardiovascular mechano-epigenetics emerges as an attractive field of study. Given the rapid advances in this emergent field of research, this short review aims to provide an analysis of the state of knowledge of force-induced epigenetic changes in the cardiovascular field.
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Affiliation(s)
- Pamela Swiatlowska
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
| | - Thomas Iskratsch
- School of Engineering and Materials Science, Queen Mary University of London, London, UK.
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Xin W, Tu S, Yi S, Xiong Y, Fang K, Sun G, Xiao W. Clinical significance of tumor suppressor genes methylation in circulating tumor DNA of patients with pancreatic cancer. Gene 2024; 897:148078. [PMID: 38097094 DOI: 10.1016/j.gene.2023.148078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/14/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) has emerged as a potential diagnostic and prognostic biomarker in various tumors. However, the role of tumor suppressor genes (TSGs) methylation in ctDNA of patients with pancreatic cancer (PC) remains largely unclear. METHODS Patients with PC (n = 43), pancreatic benign diseases (n = 39), and healthy controls (n = 20) were enrolled in the study. Quantitative analysis of methylation pattern of five candidate TSGs including NPTX2, RASSF1A, EYA2, p16, and ppENK in ctDNA was performed by next generation sequencing (NGS). The diagnostic performances of these 5-TSGs methylation were assessed by the operating characteristic (ROC) curve and clinicopathological features correlation analysis. Meanwhile, the changes in methylation levels of these 5-TSGs on the 7th postoperative day were evaluated in 23 PC patients who underwent radical resection. RESULTS The methylation levels of RASSF1A, EYA2, ppENK and p16 genes in patients with PC were significantly higher than those in healthy controls. EYA2, p16 and ppENK genes showed significantly hypermethylation in PC than those in pancreatic benign diseases. NPTX2, RASSF1A, EYA2, p16 and ppENK genes showed significantly hypermethylation in pancreatic benign diseases than those in healthy controls (P < 0.05). The methylation levels of these 5 candidate TSGs were not correlated with the tumor size, nerve invasion, lymph node metastasis and TNM stage of PC. The AUC of these biomarkers for diagnosis of PC ranged from 0.65 to 0.96. The AUC values of these methylated genes and CpG sites for differentiating malignant and benign pancreatic diseases were ranging from 0.68 to 0.92. Combined the hypermethylated genes improved the detective ability of PC than single gene. The methylation levels of NPTX2, EYA2 and ppENK genes were significantly decreased after radical resection of PC. CONCLUSION Quantitative analysis of methylation pattern of NPTX2, RASSF1A, EYA2, p16 and ppENK in ctDNA by NGS could be a valuable non-invasive tool for detection and monitoring of PC.
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Affiliation(s)
- WanPeng Xin
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Shuju Tu
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Siqing Yi
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Yuanpeng Xiong
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Kang Fang
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Gen Sun
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Weidong Xiao
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China; Institute of Digestive Surgery, Nanchang University, Nanchang, Jiangxi, China.
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Zeng C, Song X, Zhang Z, Cai Q, Cai J, Horbinski C, Hu B, Cheng SY, Zhang W. Dissection of transcriptomic and epigenetic heterogeneity of grade 4 gliomas: implications for prognosis. Acta Neuropathol Commun 2023; 11:133. [PMID: 37580817 PMCID: PMC10426201 DOI: 10.1186/s40478-023-01619-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/09/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Grade 4 glioma is the most aggressive and currently incurable brain tumor with a median survival of one year in adult patients. Elucidating novel transcriptomic and epigenetic contributors to the molecular heterogeneity underlying its aggressiveness may lead to improved clinical outcomes. METHODS To identify grade 4 glioma -associated 5-hydroxymethylcytosine (5hmC) and transcriptomic features as well as their cross-talks, genome-wide 5hmC and transcriptomic profiles of tissue samples from 61 patients with grade 4 gliomas and 9 normal controls were obtained for differential and co-regulation/co-modification analyses. Prognostic models on overall survival based on transcriptomic features and the 5hmC modifications summarized over genic regions (promoters, gene bodies) and brain-derived histone marks were developed using machine learning algorithms. RESULTS Despite global reduction, the majority of differential 5hmC features showed higher modification levels in grade 4 gliomas as compared to normal controls. In addition, the bi-directional correlations between 5hmC modifications over promoter regions or gene bodies and gene expression were greatly disturbed in grade 4 gliomas regardless of IDH1 mutation status. Phenotype-associated co-regulated 5hmC-5hmC modules and 5hmC-mRNA modules not only are enriched with different molecular pathways that are indicative of the pathogenesis of grade 4 gliomas, but also are of prognostic significance comparable to IDH1 mutation status. Lastly, the best-performing 5hmC model can predict patient survival at a much higher accuracy (c-index = 74%) when compared to conventional prognostic factor IDH1 (c-index = 57%), capturing the molecular characteristics of tumors that are independent of IDH1 mutation status and gene expression-based molecular subtypes. CONCLUSIONS The 5hmC-based prognostic model could offer a robust tool to predict survival in patients with grade 4 gliomas, potentially outperforming existing prognostic factors such as IDH1 mutations. The crosstalk between 5hmC and gene expression revealed another layer of complexity underlying the molecular heterogeneity in grade 4 gliomas, offering opportunities for identifying novel therapeutic targets.
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Affiliation(s)
- Chang Zeng
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA
| | - Xiao Song
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA
| | - Zhou Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA
| | - Qinyun Cai
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA
| | - Jiajun Cai
- Huashan Hospital, Fudan University, 12 Wulumuqi Rd., Shanghai, 200040, China
| | - Craig Horbinski
- Department of Pathology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, USA
- The Robert H. Lurie Comprehensive Cancer Center and Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA
| | - Bo Hu
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA
- The Robert H. Lurie Comprehensive Cancer Center and Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA
| | - Shi-Yuan Cheng
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA.
- The Robert H. Lurie Comprehensive Cancer Center and Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA.
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA.
- Department of Pathology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, USA.
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Liu W, Jin KM, Zhang MH, Bao Q, Liu M, Xu D, Wang K, Xing BC. Recurrence Prediction by Circulating Tumor DNA in the Patient with Colorectal Liver Metastases After Hepatectomy: A Prospective Biomarker Study. Ann Surg Oncol 2023; 30:4916-4926. [PMID: 37219651 DOI: 10.1245/s10434-023-13362-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/02/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND The recurrence rate after hepatic resection of colorectal liver metastases (CRLM) remains high. This study aimed to investigate postoperative circulating tumor DNA (ctDNA) based on ultra-deep next-generation sequencing (NGS) to predict patient recurrence and survival. METHODS Using the high-throughput NGS method tagged with a dual-indexed unique molecular identifier, named the CRLM-specific 25-gene panel (J25), this study sequenced ctDNA in peripheral blood samples collected from 134 CRLM patients who underwent hepatectomy after postoperative day 6. RESULTS Of 134 samples, 42 (31.3%) were shown to be ctDNA-positive, and 37 resulted in recurrence. Kaplan-Meier survival analysis showed that disease-free survival (DFS) in the ctDNA-positive subgroup was significantly shorter than in the ctDNA-negative subgroup (hazard ratio [HR], 2.96; 95% confidence interval [CI], 1.91-4.6; p < 0.05). When the 42 ctDNA-positive samples were further divided by the median of the mean allele frequency (AF, 0.1034%), the subgroup with higher AFs showed a significantly shorter DFS than the subgroup with lower AFs (HR, 1.98; 95% CI, 1.02-3.85; p < 0.05). The ctDNA-positive patients who received adjuvant chemotherapy longer than 2 months showed a significantly longer DFS than those who received treatment for 2 months or less (HR, 0.377; 95% CI, 0.189-0.751; p < 0.05). Uni- and multivariable Cox regression indicated two factors independently correlated with prognosis: ctDNA positivity and no preoperative chemotherapy. CONCLUSION The study demonstrated that ctDNA status 6 days postoperatively could sensitively and accurately predict recurrence for patients with CRLM using the J25 panel.
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Affiliation(s)
- Wei Liu
- Key Laboratory of Carcinogenesis and Translational Research, Hepatopancreatobiliary Surgery Department I, Ministry of Education, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Ke-Min Jin
- Key Laboratory of Carcinogenesis and Translational Research, Hepatopancreatobiliary Surgery Department I, Ministry of Education, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Meng-Huan Zhang
- GloriousMed Clinical Laboratory (Shanghai) Co., Ltd., Shanghai, People's Republic of China
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, People's Republic of China
| | - Quan Bao
- Key Laboratory of Carcinogenesis and Translational Research, Hepatopancreatobiliary Surgery Department I, Ministry of Education, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Ming Liu
- Key Laboratory of Carcinogenesis and Translational Research, Hepatopancreatobiliary Surgery Department I, Ministry of Education, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Da Xu
- Key Laboratory of Carcinogenesis and Translational Research, Hepatopancreatobiliary Surgery Department I, Ministry of Education, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Kun Wang
- Key Laboratory of Carcinogenesis and Translational Research, Hepatopancreatobiliary Surgery Department I, Ministry of Education, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing, People's Republic of China.
| | - Bao-Cai Xing
- Key Laboratory of Carcinogenesis and Translational Research, Hepatopancreatobiliary Surgery Department I, Ministry of Education, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing, People's Republic of China.
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Mo S, Ye L, Wang D, Han L, Zhou S, Wang H, Dai W, Wang Y, Luo W, Wang R, Xu Y, Cai S, Liu R, Wang Z, Cai G. Early Detection of Molecular Residual Disease and Risk Stratification for Stage I to III Colorectal Cancer via Circulating Tumor DNA Methylation. JAMA Oncol 2023; 9:770-778. [PMID: 37079312 PMCID: PMC10119774 DOI: 10.1001/jamaoncol.2023.0425] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 12/21/2022] [Indexed: 04/21/2023]
Abstract
Importance Detection of molecular residual disease and risk stratification as early as possible may improve the treatment of patients with cancer. Efficient pragmatic tests are therefore required. Objective To measure circulating tumor DNA (ctDNA) with 6 DNA methylation markers in blood samples and to evaluate the association of the presence of ctDNA with colorectal cancer (CRC) recurrence throughout the disease course. Design, Setting, and Participants In this multicenter prospective longitudinal cohort study performed from December 12, 2019, to February 28, 2022, 350 patients with stage I to III CRC were recruited from 2 hospitals for collection of blood samples before and after surgery, during and after adjuvant chemotherapy, and every 3 months for up to 2 years. A multiplex, ctDNA methylation, quantitative polymerase chain reaction assay was used to detect ctDNA in plasma samples. Results A total of 299 patients with stage I to III CRC were evaluated. Of 296 patients with preoperative samples, 232 (78.4%) tested positive for any of the 6 ctDNA methylation markers. A total of 186 patients (62.2%) were male, and the mean (SD) age was 60.1 (10.3) years. At postoperative month 1, ctDNA-positive patients were 17.5 times more likely to relapse than were ctDNA-negative patients (hazard ratio [HR], 17.5; 95% CI, 8.9-34.4; P < .001). The integration of ctDNA and carcinoembryonic antigen tests showed risk stratification for recurrence with an HR of 19.0 (95% CI, 8.9-40.7; P < .001). Furthermore, ctDNA status at postoperative month 1 was strongly associated with prognosis in patients treated with adjuvant chemotherapy of different durations and intensities. After adjuvant chemotherapy, ctDNA-positive patients had a significantly shorter recurrence-free survival than did the ctDNA-negative patients (HR, 13.8; 95% CI, 5.9-32.1; P < .001). Longitudinal ctDNA analysis after the postdefinitive treatment showed a discriminating effect in that ctDNA-positive patients had poorer recurrence-free survival than did the ctDNA-negative patients (HR, 20.6; 95% CI, 9.5-44.9; P < .001). The discriminating effect was enhanced (HR, 68.8; 95% CI, 18.4-257.7; P < .001) when ctDNA status was maintained longitudinally. Postdefinitive treatment analysis detected CRC recurrence earlier than radiologically confirmed recurrence, with a median lead time of 3.3 months (IQR, 0.5-6.5 months). Conclusions and Relevance The findings of this cohort study suggest that longitudinal assessment of ctDNA methylation may enable the early detection of recurrence, potentially optimizing risk stratification and postoperative treatment of patients with CRC.
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Affiliation(s)
- Shaobo Mo
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Li Ye
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dongyang Wang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lingyu Han
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shuang Zhou
- Singlera Genomics (Shanghai) Ltd, Shanghai, China
| | - Hui Wang
- Singlera Genomics (Shanghai) Ltd, Shanghai, China
| | - Weixing Dai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yichao Wang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenqin Luo
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Renjie Wang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Sanjun Cai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Rui Liu
- Singlera Genomics (Shanghai) Ltd, Shanghai, China
| | - Zheng Wang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guoxiang Cai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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11
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Zhang Z, Wang W, Zhang Y, You X, Wu J. A potential link between aberrant expression of ECRG4 and atrial fibrillation. Front Oncol 2023; 13:1031128. [PMID: 36910669 PMCID: PMC9992723 DOI: 10.3389/fonc.2023.1031128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 02/08/2023] [Indexed: 02/24/2023] Open
Abstract
Esophageal cancer-related gene-4 (ECRG4), a 148-amino acid propertied and new tumor suppressor, is initially cloned from the normal esophageal epithelium. ECRG4 was found to be expressed not only in esophageal tissues but also in cardiomyocytes. Previous studies demonstrated that ECRG4 is constitutively expressed in esophageal epithelial cells, and its degree of downregulation is directly proportional to prognosis in patients with esophageal cancer. In the heart, ECRG4 shows greater expression in the atria than in the ventricles, which accounts for its heterogeneity. Downregulation of ECRG4 expression level correlates with esophageal cancer, as well as myocardial injuries and arrhythmias. As a result, this review summarizes the possible susceptibility gene, ECRG4 and its associated molecular mechanisms in cancer patients with atrial fibrillation and myocardial injury. The review begins by describing ECRG4's biological background, discusses its expression in the cardiovascular system, lists the clinical and animal research related to the downregulation of ECRG4 in atrial fibrillation, and focuses on its potential role in atrial fibrillation. Downregulation of ECRG4 may increase the risk of atrial fibrillation by affecting ion channels, MMPs expression and inflammatory response. We will then discuss how ECRG4 can be used in the treatment of tumors and arrhythmias, and provide a novel possible strategy to reduce the occurrence of perioperative cardiovascular adverse events in patients with tumors such as esophageal cancer and gastric cancer.
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Affiliation(s)
- Zuojing Zhang
- Department of Anesthesiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Wei Wang
- Department of Anesthesiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Yuxin Zhang
- Department of Anesthesiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Xingji You
- School of Medicine, Shanghai University, Shanghai, China
| | - Jingxiang Wu
- Department of Anesthesiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
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12
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Telekes A, Horváth A. The Role of Cell-Free DNA in Cancer Treatment Decision Making. Cancers (Basel) 2022; 14:6115. [PMID: 36551600 PMCID: PMC9776613 DOI: 10.3390/cancers14246115] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
The aim of this review is to evaluate the present status of the use of cell-free DNA and its fraction of circulating tumor DNA (ctDNA) because this year July 2022, an ESMO guideline was published regarding the application of ctDNA in patient care. This review is for clinical oncologists to explain the concept, the terms used, the pros and cons of ctDNA; thus, the technical aspects of the different platforms are not reviewed in detail, but we try to help in navigating the current knowledge in liquid biopsy. Since the validated and adequately sensitive ctDNA assays have utility in identifying actionable mutations to direct targeted therapy, ctDNA may be used for this soon in routine clinical practice and in other different areas as well. The cfDNA fragments can be obtained by liquid biopsy and can be used for diagnosis, prognosis, and selecting among treatment options in cancer patients. A great proportion of cfDNA comes from normal cells of the body or from food uptake. Only a small part (<1%) of it is related to tumors, originating from primary tumors, metastatic sites, or circulating tumor cells (CTCs). Soon the data obtained from ctDNA may routinely be used for finding minimal residual disease, detecting relapse, and determining the sites of metastases. It might also be used for deciding appropriate therapy, and/or emerging resistance to the therapy and the data analysis of ctDNA may be combined with imaging or other markers. However, to achieve this goal, further clinical validations are inevitable. As a result, clinicians should be aware of the limitations of the assays. Of course, several open questions are still under research and because of it cfDNA and ctDNA testing are not part of routine care yet.
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Affiliation(s)
- András Telekes
- Omnimed-Etosz, Ltd., 81 Széher Rd., 1021 Budapest, Hungary
- Semmelweis University, 26. Üllői Rd., 1085 Budapest, Hungary
| | - Anna Horváth
- Department of Internal Medicine and Haematology, Semmelweis University, 46. Szentkirályi Rd., 1088 Budapest, Hungary
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13
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Liu Z, Han Y, Dang Q, Xu H, Zhang Y, Duo M, Lv J, Li H, Kong Y, Han X. Roles of circulating tumor DNA in PD-1/PD-L1 immune checkpoint Inhibitors: Current evidence and future directions. Int Immunopharmacol 2022; 111:109173. [PMID: 35998502 DOI: 10.1016/j.intimp.2022.109173] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/11/2022] [Accepted: 08/14/2022] [Indexed: 12/18/2022]
Abstract
Circulating tumor DNA (ctDNA) sequencing holds considerable promise for early diagnosis and detection of surveillance and minimal residual disease. Blood ctDNA monitors specific cancers by detecting the alterations found in cancer cells, such as apoptosis and necrosis. Due to the short half-life, ctDNA reflects the actual burden of other treatments on tumors. In addition, ctDNA might be preferable to monitor tumor development and treatment compared with invasive tissue biopsy. ctDNA-based liquid biopsy brings remarkable strength to targeted therapy and precision medicine. Notably, multiple ctDNA analysis platforms have been broadly applied in clinical immunotherapy. Through targeted sequencing, early variations in ctDNA could predict response to immune checkpoint inhibitor (ICI). Several studies have demonstrated a correlation between ctDNA kinetics and anti-PD1 antibodies. The need for further research and development remains, although this biomarker holds significant prospects for early cancer detection. This review focuses on describing the basis of ctDNA and its current utilities in oncology and immunotherapy, either for clinical management or early detection, highlighting its advantages and inherent limitations.
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Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China.
| | - Yilin Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Qin Dang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Hui Xu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Mengjie Duo
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jinxiang Lv
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Huanyun Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ying Kong
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China.
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14
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Electrochemical Biosensors for Circulating Tumor DNA Detection. BIOSENSORS 2022; 12:bios12080649. [PMID: 36005048 PMCID: PMC9406149 DOI: 10.3390/bios12080649] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 11/24/2022]
Abstract
Early diagnosis and treatment have always been highly desired in the fight against cancer, and detection of circulating tumor DNA (ctDNA) has recently been touted as highly promising for early cancer-screening. Consequently, the detection of ctDNA in liquid biopsy is gaining much attention in the field of tumor diagnosis and treatment, which has also attracted research interest from industry. However, it is difficult to achieve low-cost, real-time, and portable measurement of ctDNA in traditional gene-detection technology. Electrochemical biosensors have become a highly promising solution to ctDNA detection due to their unique advantages such as high sensitivity, high specificity, low cost, and good portability. Therefore, this review aims to discuss the latest developments in biosensors for minimally invasive, rapid, and real-time ctDNA detection. Various ctDNA sensors are reviewed with respect to their choices of receptor probes, designs of electrodes, detection strategies, preparation of samples, and figures of merit, sorted by type of electrode surface recognition elements. The development of biosensors for the Internet of Things, point-of-care testing, big data, and big health is analyzed, with a focus on their portable, real-time, and non-destructive characteristics.
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15
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Meng W, Zhang W, Yang S, Dou X, Liu Y, Li H, Liu J, Jin T, Li B. Analysis of pharmacogenomic very important pharmacogenomic variants: CYP3A5, ACE, PTGS2 and NAT2 genes in Chinese Bai population. Per Med 2022; 19:403-410. [PMID: 35801384 DOI: 10.2217/pme-2021-0157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: Our study aimed to screen the genotype frequencies of very important pharmacogenomic (VIP) mutations and identify their differences between Bai and other populations. Materials & methods: We selected 66 VIP variants from PharmGKB (www.pharmgkb.org/) for genotyping. χ2 test was used to identify differences in loci between these populations and Fst values of Bai and the other 26 populations were analyzed. Results: Our study showed that the frequencies of SNPs of CYP3A5, ACE, PTGS2 and NAT2 differed significantly from those of the other 26 populations. At the same time, we found that some VIP variants may affect the metabolism of drugs and the genetic relationship between the Bai population and East Asian populations was found to be the closest. Conclusion: By comparing the genotype frequencies of different populations, the loci with significant differences were identified and discussed, providing a theoretical basis for individualized drug use in the Bai ethnic population.
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Affiliation(s)
- Wenting Meng
- Key Laboratory of Resource Biology & Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 229 TaiBai North Road, Xi'an, 710069, China.,Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Wenjie Zhang
- Key Laboratory of Resource Biology & Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 229 TaiBai North Road, Xi'an, 710069, China.,Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Shuangyu Yang
- Key Laboratory of Resource Biology & Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 229 TaiBai North Road, Xi'an, 710069, China.,Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Xia Dou
- Key Laboratory of Resource Biology & Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 229 TaiBai North Road, Xi'an, 710069, China.,Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Yuanwei Liu
- Key Laboratory of Resource Biology & Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 229 TaiBai North Road, Xi'an, 710069, China.,Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Haiyue Li
- Key Laboratory of Resource Biology & Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 229 TaiBai North Road, Xi'an, 710069, China.,Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Jianfeng Liu
- Key Laboratory of Resource Biology & Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 229 TaiBai North Road, Xi'an, 710069, China.,Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Tianbo Jin
- Key Laboratory of Resource Biology & Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 229 TaiBai North Road, Xi'an, 710069, China.,Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Bin Li
- Key Laboratory of Resource Biology & Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 229 TaiBai North Road, Xi'an, 710069, China.,Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
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16
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Wu HJ, Chu PY. Current and Developing Liquid Biopsy Techniques for Breast Cancer. Cancers (Basel) 2022; 14:2052. [PMID: 35565189 PMCID: PMC9105073 DOI: 10.3390/cancers14092052] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is the most commonly diagnosed cancer and leading cause of cancer mortality among woman worldwide. The techniques of diagnosis, prognosis, and therapy monitoring of breast cancer are critical. Current diagnostic techniques are mammography and tissue biopsy; however, they have limitations. With the development of novel techniques, such as personalized medicine and genetic profiling, liquid biopsy is emerging as the less invasive tool for diagnosing and monitoring breast cancer. Liquid biopsy is performed by sampling biofluids and extracting tumor components, such as circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), cell-free mRNA (cfRNA) and microRNA (miRNA), proteins, and extracellular vehicles (EVs). In this review, we summarize and focus on the recent discoveries of tumor components and biomarkers applied in liquid biopsy and novel development of detection techniques, such as surface-enhanced Raman spectroscopy (SERS) and microfluidic devices.
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Affiliation(s)
- Hsing-Ju Wu
- Research Assistant Center, Show Chwan Memorial Hospital, Changhua 500, Taiwan;
- Department of Medical Research, Chang Bing Show Chwan Memorial Hospital, Lukang Town, Changhua 505, Taiwan
- Department of Biology, National Changhua University of Education, Changhua 500, Taiwan
| | - Pei-Yi Chu
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Department of Pathology, Show Chwan Memorial Hospital, Changhua 500, Taiwan
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan
- Department of Health Food, Chung Chou University of Science and Technology, Changhua 510, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
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17
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Biomimetic Nanoscale Materials for Skin Cancer Therapy and Detection. J Skin Cancer 2022; 2022:2961996. [PMID: 35433050 PMCID: PMC9010180 DOI: 10.1155/2022/2961996] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/29/2022] [Indexed: 02/06/2023] Open
Abstract
Skin cancer has developed as one of the most common types of cancer in the world, with a significant impact on public health impact and the economy. Nanotechnology methods for cancer treatment are appealing since they allow for the effective transport of medicines and other biologically active substances to specific tissues while minimizing harmful consequences. It is one of the most significant fields of research for treating skin cancer. Various nanomaterials have been employed in skin cancer therapy. The current review will summarize numerous methods of treating and diagnosing skin cancer in the earliest stages. There are numerous skin cancer indicators available for the prompt diagnosis of this type of disease. Traditional approaches to skin cancer diagnosis are explored, as are their shortcomings. Electrochemical and optical biosensors for skin cancer diagnosis and management were also discussed. Finally, various difficulties concerning the cost and ease of use of innovative methods should be addressed and overcome.
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Active demethylation upregulates CD147 expression promoting non-small cell lung cancer invasion and metastasis. Oncogene 2022; 41:1780-1794. [PMID: 35132181 PMCID: PMC8933279 DOI: 10.1038/s41388-022-02213-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 01/07/2022] [Accepted: 01/26/2022] [Indexed: 12/20/2022]
Abstract
Non-small cell lung cancer (NSCLC) is a fatal disease, and its metastatic process is poorly understood. Although aberrant methylation is involved in tumor progression, the mechanisms underlying dynamic DNA methylation remain to be elucidated. It is significant to study the molecular mechanism of NSCLC metastasis and identify new biomarkers for NSCLC early diagnosis. Here, we performed MeDIP-seq and hMeDIP-seq analyses to detect the genes regulated by dynamic DNA methylation. Comparison of the 5mC and 5hmC sites revealed that the CD147 gene underwent active demethylation in NSCLC tissues compared with normal tissues, and this demethylation upregulated CD147 expression. Significantly high levels of CD147 expression and low levels of promoter methylation were observed in NSCLC tissues. Then, we identified the CD147 promoter as a target of KLF6, MeCP2, and DNMT3A. Treatment of cells with TGF-β triggered active demethylation involving loss of KLF6/MeCP2/DNMT3A and recruitment of Sp1, Tet1, TDG, and SMAD2/3 transcription complexes. A dCas9-SunTag-DNMAT3A-sgCD147-targeted methylation system was constructed to reverse CD147 expression. The targeted methylation system downregulated CD147 expression and inhibited NSCLC proliferation and metastasis in vitro and in vivo. Accordingly, we used cfDNA to detect the levels of CD147 methylation in NSCLC tissues and found that the CD147 methylation levels exhibited an inverse relationship with tumor size, lymphatic metastasis, and TNM stage. In conclusion, this study clarified the mechanism of active demethylation of CD147 and suggested that the targeted methylation of CD147 could inhibit NSCLC invasion and metastasis, providing a highly promising therapeutic target for NSCLC.
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Tserpeli V, Stergiopoulou D, Londra D, Giannopoulou L, Buderath P, Balgkouranidou I, Xenidis N, Grech C, Obermayr E, Zeillinger R, Pavlakis K, Rampias T, Kakolyris S, Kasimir-Bauer S, Lianidou ES. Prognostic Significance of SLFN11 Methylation in Plasma Cell-Free DNA in Advanced High-Grade Serous Ovarian Cancer. Cancers (Basel) 2021; 14:cancers14010004. [PMID: 35008168 PMCID: PMC8750111 DOI: 10.3390/cancers14010004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/08/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
Background: Epigenetic alterations in ctDNA are highly promising as a source of novel potential liquid biopsy biomarkers and comprise a very promising liquid biopsy approach in ovarian cancer, for early diagnosis, prognosis and response to treatment. Methods: In the present study, we examined the methylation status of six gene promoters (BRCA1, CST6, MGMT, RASSF10, SLFN11 and USP44) in high-grade serous ovarian cancer (HGSOC). We evaluated the prognostic significance of DNA methylation of these six gene promoters in primary tumors (FFPEs) and plasma cfDNA samples from patients with early, advanced and metastatic HGSOC. Results: We report for the first time that the DNA methylation of SLFN11 in plasma cfDNA was significantly correlated with worse PFS (p = 0.045) in advanced stage HGSOC. Conclusions: Our results strongly indicate that SLFN11 epigenetic inactivation could be a predictor of resistance to platinum drugs in ovarian cancer. Our results should be further validated in studies based on a larger cohort of patients, in order to further explore whether the DNA methylation of SLFN11 promoter could serve as a potential prognostic DNA methylation biomarker and a predictor of resistance to platinum-based chemotherapy in ovarian cancer.
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Affiliation(s)
- Victoria Tserpeli
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (V.T.); (D.S.); (D.L.); (L.G.)
| | - Dimitra Stergiopoulou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (V.T.); (D.S.); (D.L.); (L.G.)
| | - Dora Londra
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (V.T.); (D.S.); (D.L.); (L.G.)
| | - Lydia Giannopoulou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (V.T.); (D.S.); (D.L.); (L.G.)
| | - Paul Buderath
- Department of Gynecology and Obstetrics, University Hospital of Essen, University of Duisburg-Essen, Hufelandstrasse 55, D-45122 Essen, Germany; (P.B.); (S.K.-B.)
| | - Ioanna Balgkouranidou
- Department of Oncology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (I.B.); (N.X.); (S.K.)
| | - Nikolaos Xenidis
- Department of Oncology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (I.B.); (N.X.); (S.K.)
| | - Christina Grech
- Department of Obstetrics and Gynecology, Medical University of Vienna, 1090 Vienna, Austria; (C.G.); (E.O.); (R.Z.)
| | - Eva Obermayr
- Department of Obstetrics and Gynecology, Medical University of Vienna, 1090 Vienna, Austria; (C.G.); (E.O.); (R.Z.)
| | - Robert Zeillinger
- Department of Obstetrics and Gynecology, Medical University of Vienna, 1090 Vienna, Austria; (C.G.); (E.O.); (R.Z.)
| | - Kitty Pavlakis
- Pathology Department, IASO Women’s Hospital, 15123 Athens, Greece;
| | - Theodoros Rampias
- Basic Research Center, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece;
| | - Stylianos Kakolyris
- Department of Oncology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (I.B.); (N.X.); (S.K.)
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, University of Duisburg-Essen, Hufelandstrasse 55, D-45122 Essen, Germany; (P.B.); (S.K.-B.)
| | - Evi S. Lianidou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (V.T.); (D.S.); (D.L.); (L.G.)
- Correspondence: ; Tel.: +30-210-7274311
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Mishra S, Jeon J, Kang JK, Song SH, Kim TY, Ban C, Choi H, Kim Y, Kim M, Park JW. Direct Detection of Low Abundance Genes of Single Point Mutation. NANO LETTERS 2021; 21:9061-9068. [PMID: 34672610 DOI: 10.1021/acs.nanolett.1c02728] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cell-free DNA (cfDNA) analysis, specifically circulating tumor DNA (ctDNA) analysis, provides enormous opportunities for noninvasive early assessment of cancers. To date, PCR-based methods have led this field. However, the limited sensitivity/specificity of PCR-based methods necessitates the search for new methods. Here, we describe a direct approach to detect KRAS G12D mutated genes in clinical ctDNA samples with the utmost LOD and sensitivity/specificity. In this study, MutS protein was immobilized on the tip of an atomic force microscope (AFM), and the protein sensed the mismatched sites of the duplex formed between the capture probe on the surface and mutated DNA. A noteworthy LOD (3 copies, 0.006% allele frequency) was achieved, along with superb sensitivity/specificity (100%/100%). These observations demonstrate that force-based AFM, in combination with the protein found in nature and properly designed capture probes/blockers, represents an exciting new avenue for ctDNA analysis.
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Affiliation(s)
- Sourav Mishra
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Jinseong Jeon
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Jun-Kyu Kang
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Republic of Korea
| | - Sang-Hyun Song
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Republic of Korea
| | - Tae-You Kim
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hayoung Choi
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Yonggoo Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Myungshin Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Joon Won Park
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
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21
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Ghalkhani E, Akbari MT, Izadi P, Mahmoodzadeh H, Kamali F. Assessment of DAPK1 and CAVIN3 Gene Promoter Methylation in Breast Invasive Ductal Carcinoma and Metastasis. CELL JOURNAL 2021; 23:397-405. [PMID: 34455714 PMCID: PMC8405083 DOI: 10.22074/cellj.2021.7251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/26/2020] [Indexed: 12/15/2022]
Abstract
Objective Metastasis might be latent or occur several years after primary tumor removal. Currently used methods for detection of distant metastasis have still some limitations. Blood tests may improve sensitivity and specificity of currently used screening procedures. The present study was designed to investigate promoter methylation status of DAPK1 and CAVIN3 genes in plasma circulating free DNA (cfDNA) samples in Iranian invasive ductal carcinoma (IDC) patients. We also investigated association of two gene promoter methylations with breast cancer (BC) and metastatic BC was also assessed. Materials and Methods In this case-control study, MethySYBR assay was performed to determine DAPK1 and CAVIN3 promoter methylation status in breast IDC from 90 patients and 30 controls. Based on clinicopathological information, patient samples subdivided into stage I, II/III and IV groups (each group contained 30 individuals). Results According to the results an increased promoter methylation level of the DAPK1 gene in BC patients was observed. It was found that as disease progressed, the percentage of methylation was changed while it was not significant. Methylation changes in metastatic and non-metastatic BC revealed that methylation levels were significantly increased in metastatic than non-metastatic group. Analysis revealed that promoter methylation of CAVIN3 gene in BC patients was significantly increased. The observed methylation changes from less to more invasive stages were not significant in the CAVIN3 gene. Moreover, promoter methylation was changed in metastatic rather than non-metastatic condition, although it was not significant. Conclusion Promoter hypermethylation of c and CAVIN3 genes in plasma are associated with the risk of BC and they can be potential diagnostic biomarkers along with current methods. Additionally, association of aberrant DAPK1 promoter methylation with metastasis suggests its potential usage as a non-invasive strategy for metastatic BC diagnosis.
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Affiliation(s)
- Esmat Ghalkhani
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Taghi Akbari
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Pantea Izadi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Habibollah Mahmoodzadeh
- Department of Surgery, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Kamali
- Iran National Tumor Bank, Cancer Institute of Iran, Tehran, University of Medical Sciences, Tehran, Iran
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22
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Chen D, Wang M, Guo Y, Wu W, Ji X, Dou X, Tang H, Zong Z, Zhang X, Xiong D. An aberrant DNA methylation signature for predicting the prognosis of head and neck squamous cell carcinoma. Cancer Med 2021; 10:5936-5947. [PMID: 34313009 PMCID: PMC8419750 DOI: 10.1002/cam4.4142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 05/28/2021] [Accepted: 06/24/2021] [Indexed: 11/09/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a common malignancy worldwide with a poor prognosis. DNA methylation is an epigenetic modification that plays a critical role in the etiology and pathogenesis of HNSCC. The current study aimed to develop a predictive methylation signature based on bioinformatics analysis to improve the prognosis and optimize therapeutic outcome in HNSCC. Clinical information and methylation sequencing data of patients with HNSCC were downloaded from The Cancer Genome Atlas database. The R package was used to identify differentially methylated genes (DMGs) between HNSCC and adjacent normal tissues. We identified 22 DMGs associated with 246 differentially methylated sites. Patients with HNSCC were classified into training and test groups. Cox regression analysis was used to build a risk score formula based on the five methylation sites (cg26428455, cg13754259, cg17421709, cg19229344, and cg11668749) in the training group. The Kaplan–Meier survival curves showed that the overall survival (OS) rates were significantly different between the high‐ and low‐risk groups sorted by the signature in the training group (median: 1.38 vs. 1.57 years, log‐rank test, p < 0.001). The predictive power was then validated in the test group (median: 1.34 vs. 1.75 years, log‐rank test, p < 0.001). The area under the receiver operating characteristic curve (area under the curve) based on the signature for predicting the 5‐year survival rates, was 0.7 in the training and 0.73 in test groups, respectively. The results of multivariate Cox regression analysis showed that the riskscore (RS) signature based on the five methylation sites was an independent prognostic tool for OS prediction in patients. In addition, a predictive nomogram model that incorporated the RS signature and patient clinical information was developed. The innovative methylation signature‐based model developed in our study represents a robust prognostic tool for guiding clinical therapy and predicting the OS in patients with HNSCC.
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Affiliation(s)
- Dayang Chen
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Mengmeng Wang
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China.,School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Ying Guo
- Department of Clinical Laboratory, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Wei Wu
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Xiang Ji
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Xiaowen Dou
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Huamei Tang
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Zengyan Zong
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China.,School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Xiuming Zhang
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China.,School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Dan Xiong
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China.,School of Medicine, Anhui University of Science and Technology, Huainan, China
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23
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Wang D, O'Rourke D, Sanchez-Garcia JF, Cai T, Scheuenpflug J, Feng Z. Development of a liquid biopsy based purely quantitative digital droplet PCR assay for detection of MLH1 promoter methylation in colorectal cancer patients. BMC Cancer 2021; 21:797. [PMID: 34243735 PMCID: PMC8272385 DOI: 10.1186/s12885-021-08497-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/11/2021] [Indexed: 01/05/2023] Open
Abstract
Background MutL Homolog 1 (MLH1) promotor methylation is associated with microsatellite instability high colorectal cancer (CRC). The strong correlation between methylation status and cancer development and progression has led to a growing interest in the use of methylation markers in circulating tumor DNA (ctDNA) for early cancer detection and longitudinal monitoring. As cancer-specific DNA methylation changes in body fluids are limited, it is particularly challenging to develop clinically applicable liquid biopsy methodologies with high sensitivity and specificity. The purpose of this study was to develop a fit-for-purpose methylation sensitive restriction enzyme (MSRE) based digital droplet PCR (ddPCR) assay to examine MLH1 promoter methylation in ctDNA in advanced CRC. Methods Primers and probes were designed to amplify CpG sites of the MLH1 promoter. Methylated and unmethylated control genomic DNA were sheared to mimic ctDNA and subjected to MSRE HpaII digestion. Plasma samples from 20 healthy donors and 28 CRC patients were analyzed with the optimized MSRE procedure using ddPCR. Results Using methylated and unmethylated controls, we optimized the conditions for HpaII enzyme digestion to ensure complete digestion and avoid false positives. Based on the results from the ddPCR assay using 1 ng circulating cell-free DNA (cfDNA) input from healthy donors or CRC samples, ROC curves were generated with an area under the curve (AUC) value of 0.965 (95% CI: 0.94, 0.99). The statistically optimal assay sensitivity and specificity was achieved when 8 positive droplets were used as acceptance criteria (78% sensitivity and 100% specificity, 95% CI: 0.45, 0.95). A tiered-based cutoff (20, 50, 80% percentile based) was applied to distinguish CRC samples with different methylation level. Conclusions Our study demonstrated that the liquid biopsy assay for MLH1 promoter methylation detection using purely quantitative ddPCR is a simple and highly sensitive procedure that provides reliable methylation detection in ctDNA. The MSRE ddPCR approach can also be applied to other genes of interest where methylation patterns could reveal clinically relevant information for future clinical biomarker and/or companion diagnostic development. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08497-x.
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Affiliation(s)
- Danyi Wang
- Global Clinical Biomarkers and Companion Diagnostics, Global Early Development, EMD Serono Research and Development Institute, Billerica, MA, USA
| | - Dennis O'Rourke
- Global Clinical Biomarkers and Companion Diagnostics, Global Early Development, EMD Serono Research and Development Institute, Billerica, MA, USA
| | - Jorge F Sanchez-Garcia
- Global Clinical Biomarkers and Companion Diagnostics, Global Early Development, EMD Serono Research and Development Institute, Billerica, MA, USA
| | - Ti Cai
- Global Clinical Biomarkers and Companion Diagnostics, Global Early Development, EMD Serono Research and Development Institute, Billerica, MA, USA
| | - Juergen Scheuenpflug
- Global Clinical Biomarkers and Companion Diagnostics, Global Early Development, Merck Biopharma, Merck KGaA, Darmstadt, Germany
| | - Zheng Feng
- Global Clinical Biomarkers and Companion Diagnostics, Global Early Development, EMD Serono Research and Development Institute, Billerica, MA, USA.
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24
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Cristall K, Bidard FC, Pierga JY, Rauh MJ, Popova T, Sebbag C, Lantz O, Stern MH, Mueller CR. A DNA methylation-based liquid biopsy for triple-negative breast cancer. NPJ Precis Oncol 2021; 5:53. [PMID: 34135468 PMCID: PMC8209161 DOI: 10.1038/s41698-021-00198-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022] Open
Abstract
Here, we present a next-generation sequencing (NGS) methylation-based blood test called methylation DETEction of Circulating Tumour DNA (mDETECT) designed for the optimal detection and monitoring of metastatic triple-negative breast cancer (TNBC). Based on a highly multiplexed targeted sequencing approach, this assay incorporates features that offer superior performance and included 53 amplicons from 47 regions. Analysis of a previously characterised cohort of women with metastatic TNBC with limited quantities of plasma (<2 ml) produced an AUC of 0.92 for detection of a tumour with a sensitivity of 76% for a specificity of 100%. mDETECTTNBC was quantitative and showed superior performance to an NGS TP53 mutation-based test carried out on the same patients and to the conventional CA15-3 biomarker. mDETECT also functioned well in serum samples from metastatic TNBC patients where it produced an AUC of 0.97 for detection of a tumour with a sensitivity of 93% for a specificity of 100%. An assay for BRCA1 promoter methylation was also incorporated into the mDETECT assay and functioned well but its clinical significance is currently unclear. Clonal Hematopoiesis of Indeterminate Potential was investigated as a source of background in control subjects but was not seen to be significant, though a link to adiposity may be relevant. The mDETECTTNBC assay is a liquid biopsy able to quantitatively detect all TNBC cancers and has the potential to improve the management of patients with this disease.
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Affiliation(s)
- Katrina Cristall
- Queen's Cancer Research Institute, Queen's University, Kingston, ON, Canada.,Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Francois-Clement Bidard
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, Paris, France.,Department of Medical Oncology, Institut Curie, Paris, France
| | - Jean-Yves Pierga
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, Paris, France.,Department of Medical Oncology, Institut Curie, Paris, France.,Université Paris Descartes, Paris, France
| | - Michael J Rauh
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Tatiana Popova
- INSERM U830 Cancer, Heterogeneity, Instability and Plasticity (CHIP), Institut Curie, Paris, France
| | - Clara Sebbag
- Department of Medical Oncology, Institut Curie, Paris, France
| | - Olivier Lantz
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, Paris, France.,INSERM CIC BT 1428, Institut Curie, Paris, France.,INSERM U932, Institut Curie, Paris, France
| | - Marc-Henri Stern
- INSERM U830 Cancer, Heterogeneity, Instability and Plasticity (CHIP), Institut Curie, Paris, France
| | - Christopher R Mueller
- Queen's Cancer Research Institute, Queen's University, Kingston, ON, Canada. .,Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada. .,Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada.
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25
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Koval AP, Blagodatskikh KA, Kushlinskii NE, Shcherbo DS. The Detection of Cancer Epigenetic Traces in Cell-Free DNA. Front Oncol 2021; 11:662094. [PMID: 33996585 PMCID: PMC8118693 DOI: 10.3389/fonc.2021.662094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/12/2021] [Indexed: 12/23/2022] Open
Abstract
Nucleic acid fragments found in blood circulation originate mostly from dying cells and carry signs pointing to specific features of the parental cell types. Deciphering these clues may be transformative for numerous research and clinical applications but strongly depends on the development and implementation of robust analytical methods. Remarkable progress has been achieved in the reliable detection of sequence alterations in cell-free DNA while decoding epigenetic information from methylation and fragmentation patterns requires more sophisticated approaches. This review discusses the currently available strategies for detecting and analyzing the epigenetic marks in the liquid biopsies.
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Affiliation(s)
- Anastasia P Koval
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Konstantin A Blagodatskikh
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nikolay E Kushlinskii
- Laboratory of Clinical Biochemistry, N.N. Blokhin Cancer Research Medical Center of Oncology, Moscow, Russia
| | - Dmitry S Shcherbo
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
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26
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Fernández-Domínguez IJ, Manzo-Merino J, Taja-Chayeb L, Dueñas-González A, Pérez-Cárdenas E, Trejo-Becerril C. The role of extracellular DNA (exDNA) in cellular processes. Cancer Biol Ther 2021; 22:267-278. [PMID: 33858306 DOI: 10.1080/15384047.2021.1890319] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nowadays, extracellular DNA or circulating cell-free DNA is considered to be a molecule with clinical applications (diagnosis, prognosis, monitoring of treatment responses, or patient follow-up) in diverse pathologies, especially in cancer. Nevertheless, because of its molecular characteristics, it can have many other functions. This review focuses on the participation of extracellular DNA (exDNA) in fundamental processes such as cell signaling, coagulation, immunity, evolution through horizontal transfer of genetic information, and adaptive response to inflammatory processes. A deeper understanding of its role in each of these processes will allow development of better tools to monitor and control pathologies, as well as helping to generate new therapeutic options, beyond the applicability of DNA in liquid biopsy.
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Affiliation(s)
| | | | - Lucia Taja-Chayeb
- Division of Basic Research, Instituto Nacional de Cancerología, México City
| | - Alfonso Dueñas-González
- Division of Basic Research, Instituto Nacional de Cancerología, México City.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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27
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Emerging noninvasive methylation biomarkers of cancer prognosis and drug response prediction. Semin Cancer Biol 2021; 83:584-595. [PMID: 33757849 DOI: 10.1016/j.semcancer.2021.03.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/15/2021] [Accepted: 03/16/2021] [Indexed: 12/27/2022]
Abstract
Cancer is the second leading cause of death worldwide being responsible for 9.6 million deaths in 2018. Epigenetic alterations are key in directing the aberrant expression of tumor-associated genes that drive cellular malignant transformation and cancer progression. Among epigenetic alterations, DNA methylation is the most deeply studied one in relation to environmental exposure. Tissue biopsies have traditionally been the main procedure by which a small sample of body tissue is excised to confirm cancer diagnosis or to indicate the primary site when cancer has spread. In contrast, the analysis of circulating tumor-derived material, or tumor circulome, by means of liquid biopsy of peripheral blood, urine, saliva or sputum is a noninvasive, fast and reproducible alternative to tissue biopsy. Recently, the assessment of epigenetic alterations such as DNA methylation and hydroxymethylation in circulating free DNA has been proved possible. These marks can be associated to prognosis and response to a variety of treatments including chemotherapy, hormonotherapy or immunotherapy. Epigenetic biomarkers may offer some advantages over RNA or genetic biomarkers given their stability in bodily fluids and their high tissue-specificity. While many challenges are still ahead, the unique advantages of these types of biomarkers is urging the scientific community to persevere in their clinical validation and integration into reliable prediction models. This review aims at recapitulating the emerging noninvasive DNA methylated biomarkers of importance for prediction of prognosis and drug response in cancer.
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28
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Whalley C, Payne K, Domingo E, Blake A, Richman S, Brooks J, Batis N, Spruce R, Mehanna H, Nankivell P, Beggs AD. Ultra-Low DNA Input into Whole Genome Methylation Assays and Detection of Oncogenic Methylation and Copy Number Variants in Circulating Tumour DNA. EPIGENOMES 2021; 5:6. [PMID: 33777442 PMCID: PMC7610445 DOI: 10.3390/epigenomes5010006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/06/2021] [Accepted: 02/12/2021] [Indexed: 11/28/2022] Open
Abstract
Abnormal CpG methylation in cancer is ubiquitous and generally detected in tumour specimens using a variety of techniques at a resolution encompassing single CpG loci to genome wide coverage. Analysis of samples with very low DNA inputs, such as formalin fixed (FFPE) biopsy specimens from clinical trials or circulating tumour DNA is challenging at the genome-wide level because of lack of available input. We present the results of low input experiments into the Illumina Infinium HD methylation assay on FFPE specimens and ctDNA samples. METHODS For all experiments, the Infinium HD assay for methylation was used. In total, forty-eight FFPE specimens were used at varying concentrations (lowest input 50 ng); eighteen blood derived specimens (lowest input 10 ng) and six matched ctDNA input (lowest input 10 ng)/fresh tumour specimens (lowest input 250 ng) were processed. Downstream analysis was performed in R/Bioconductor for quality control metrics and differential methylation analysis as well as copy number calls. RESULTS Correlation coefficients for CpG methylation were high at the probe level averaged R2 = 0.99 for blood derived samples and R2 > 0.96 for the FFPE samples. When matched ctDNA/fresh tumour samples were compared, R2 > 0.91 between the two. Results of differential methylation analysis did not vary significantly by DNA input in either the blood or FFPE groups. There were differences seen in the ctDNA group as compared to their paired tumour sample, possibly because of enrichment for tumour material without contaminating normal. Copy number variants observed in the tumour were generally also seen in the paired ctDNA sample with good concordance via DQ plot. CONCLUSIONS The Illumina Infinium HD methylation assay can robustly detect methylation across a range of sample types, including ctDNA, down to an input of 10 ng. It can also reliably detect oncogenic methylation changes and copy number variants in ctDNA. These findings demonstrate that these samples can now be accessed by methylation array technology, allowing analysis of these important sample types.
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Affiliation(s)
- Celina Whalley
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | - Karl Payne
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | - Enric Domingo
- Department of Oncology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; (E.D.); (A.B.)
| | - Andrew Blake
- Department of Oncology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; (E.D.); (A.B.)
| | - Susan Richman
- Pathology and Data Analytics, Leeds Institute of Medical Research, St James University Hospital, Leeds LS2 9JT, UK;
| | - Jill Brooks
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | - Nikolaos Batis
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | - Rachel Spruce
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | | | - Hisham Mehanna
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | - Paul Nankivell
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | - Andrew D. Beggs
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
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29
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Grady WM, Yu M, Markowitz SD. Epigenetic Alterations in the Gastrointestinal Tract: Current and Emerging Use for Biomarkers of Cancer. Gastroenterology 2021; 160:690-709. [PMID: 33279516 PMCID: PMC7878343 DOI: 10.1053/j.gastro.2020.09.058] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023]
Abstract
Colorectal cancer, liver cancer, stomach cancer, pancreatic cancer, and esophageal cancer are leading causes of cancer-related deaths worldwide. A fundamental trait of virtually all gastrointestinal cancers is genomic and epigenomic DNA alterations. Cancer cells acquire genetic and epigenetic alterations that drive the initiation and progression of the cancers by altering the molecular and cell biological processes of the cells. These alterations, as well as other host and microenvironment factors, ultimately mediate the clinical behavior of the precancers and cancers and can be used as biomarkers for cancer risk determination, early detection of cancer and precancer, determination of the prognosis of cancer and prediction of the response to therapy. Epigenetic alterations have emerged as one of most robust classes of biomarkers and are the basis for a growing number of clinical tests for cancer screening and surveillance.
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Affiliation(s)
- William M. Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA,Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ming Yu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
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30
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Huang HY, Li J, Tang Y, Huang YX, Chen YG, Xie YY, Zhou ZY, Chen XY, Ding SY, Luo MF, Jin CN, Zhao LS, Xu JT, Zhou Y, Lin YCD, Hong HC, Zuo HL, Hu SY, Xu PY, Li X, Huang HD. MethHC 2.0: information repository of DNA methylation and gene expression in human cancer. Nucleic Acids Res 2021; 49:D1268-D1275. [PMID: 33270889 PMCID: PMC7779066 DOI: 10.1093/nar/gkaa1104] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/18/2020] [Accepted: 11/03/2020] [Indexed: 12/25/2022] Open
Abstract
DNA methylation is an important epigenetic regulator in gene expression and has several roles in cancer and disease progression. MethHC version 2.0 (MethHC 2.0) is an integrated and web-based resource focusing on the aberrant methylomes of human diseases, specifically cancer. This paper presents an updated implementation of MethHC 2.0 by incorporating additional DNA methylomes and transcriptomes from several public repositories, including 33 human cancers, over 50 118 microarray and RNA sequencing data from TCGA and GEO, and accumulating up to 3586 manually curated data from >7000 collected published literature with experimental evidence. MethHC 2.0 has also been equipped with enhanced data annotation functionality and a user-friendly web interface for data presentation, search, and visualization. Provided features include clinical-pathological data, mutation and copy number variation, multiplicity of information (gene regions, enhancer regions, and CGI regions), and circulating tumor DNA methylation profiles, available for research such as biomarker panel design, cancer comparison, diagnosis, prognosis, therapy study and identifying potential epigenetic biomarkers. MethHC 2.0 is now available at http://awi.cuhk.edu.cn/∼MethHC.
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Affiliation(s)
- Hsi-Yuan Huang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Jing Li
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Yun Tang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Yi-Xian Huang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Yi-Gang Chen
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Yue-Yang Xie
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Zhe-Yuan Zhou
- School of Data Science, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Xin-Yi Chen
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Si-Yuan Ding
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Meng-Fan Luo
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Chen-Nan Jin
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Le-Shan Zhao
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Jia-Tong Xu
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Ying Zhou
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Yang-Chi-Dung Lin
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Hsiao-Chin Hong
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Hua-Li Zuo
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Si-Yao Hu
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Pei-Yi Xu
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Xin Li
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Hsien-Da Huang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
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Keller L, Belloum Y, Wikman H, Pantel K. Clinical relevance of blood-based ctDNA analysis: mutation detection and beyond. Br J Cancer 2021; 124:345-358. [PMID: 32968207 PMCID: PMC7852556 DOI: 10.1038/s41416-020-01047-5] [Citation(s) in RCA: 216] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 06/22/2020] [Accepted: 08/19/2020] [Indexed: 12/13/2022] Open
Abstract
Cell-free DNA (cfDNA) derived from tumours is present in the plasma of cancer patients. The majority of currently available studies on the use of this circulating tumour DNA (ctDNA) deal with the detection of mutations. The analysis of cfDNA is often discussed in the context of the noninvasive detection of mutations that lead to resistance mechanisms and therapeutic and disease monitoring in cancer patients. Indeed, substantial advances have been made in this area, with the development of methods that reach high sensitivity and can interrogate a large number of genes. Interestingly, however, cfDNA can also be used to analyse different features of DNA, such as methylation status, size fragment patterns, transcriptomics and viral load, which open new avenues for the analysis of liquid biopsy samples from cancer patients. This review will focus on the new perspectives and challenges of cfDNA analysis from mutation detection in patients with solid malignancies.
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Affiliation(s)
- Laura Keller
- University Medical Center Hamburg-Eppendorf, Institute of Tumor Biology, Martinistrasse 52, Building N27, 20246, Hamburg, Germany
| | - Yassine Belloum
- University Medical Center Hamburg-Eppendorf, Institute of Tumor Biology, Martinistrasse 52, Building N27, 20246, Hamburg, Germany
| | - Harriet Wikman
- University Medical Center Hamburg-Eppendorf, Institute of Tumor Biology, Martinistrasse 52, Building N27, 20246, Hamburg, Germany
| | - Klaus Pantel
- University Medical Center Hamburg-Eppendorf, Institute of Tumor Biology, Martinistrasse 52, Building N27, 20246, Hamburg, Germany.
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32
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Jaworski JJ, Morgan RD, Sivakumar S. Circulating Cell-Free Tumour DNA for Early Detection of Pancreatic Cancer. Cancers (Basel) 2020; 12:E3704. [PMID: 33317202 PMCID: PMC7763954 DOI: 10.3390/cancers12123704] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/04/2020] [Indexed: 01/11/2023] Open
Abstract
Pancreatic cancer is a lethal disease, with mortality rates negatively associated with the stage at which the disease is detected. Early detection is therefore critical to improving survival outcomes. A recent focus of research for early detection is the use of circulating cell-free tumour DNA (ctDNA). The detection of ctDNA offers potential as a relatively non-invasive method of diagnosing pancreatic cancer by using genetic sequencing technology to detect tumour-specific mutational signatures in blood samples before symptoms manifest. These technologies are limited by a number of factors that lower sensitivity and specificity, including low levels of detectable ctDNA in early stage disease and contamination with non-cancer circulating cell-free DNA. However, genetic and epigenetic analysis of ctDNA in combination with other standard diagnostic tests may improve early detection rates. In this review, we evaluate the genetic and epigenetic methods under investigation in diagnosing pancreatic cancer and provide a perspective for future developments.
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Affiliation(s)
- Jedrzej J. Jaworski
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK;
| | - Robert D. Morgan
- Department of Medical Oncology, Christie NHS Foundation Trust, Manchester M20 4BX, UK;
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Shivan Sivakumar
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
- Department of Medical Oncology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
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33
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Zhang R, Li Y, Yu H, Liu L, Zhu C, Zuo S, Chen Z. An aberrant DNA methylation signature for predicting hepatocellular carcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1667. [PMID: 33490179 PMCID: PMC7812168 DOI: 10.21037/atm-20-7804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background By the time they are clinically diagnosed, patients with hepatocellular carcinoma (HCC) are often at the advanced stage. DNA methylation has become a useful predictor of prognosis for cancer patients. Research on DNA methylation as a biomarker for assessing the risk of occurrence in HCC patients is limited. The purpose of this study was to develop an efficient methylation site model for predicting survival in patients with HCC. Methods DNA methylation and gene expression profile data were extracted from The Cancer Genome Atlas (TCGA) database. Markers of DNA-methylated site in two subsets (the training subset and the test subset) were identified using a random survival forest algorithm and Cox proportional hazards regression. Then, Gene Ontology annotations were applied to investigate the functions of DNA methylation signatures. Results A total of 37 hub genes containing 713 methylated sites were identified among the differentially methylated genes (DMGs) and differentially expressed genes (DEGs). Finally, seven methylation sites (cg12824782, cg24871714, cg18683774, cg22796509, cg19450025, cg10474350, and cg06511917) were identified. In the training group and the test group, the area under the curve predicting the survival of patients with HCC was 0.750 and 0.742, respectively. The seven methylation sites signature could be used to divide the patients in the training group into high- and low-risk subgroups [overall survival (OS): 2.81 vs. 2.11 years; log-rank test, P<0.05]. Then, the prediction ability of the model was validated in the test dataset through risk stratification (OS: 2.04 vs. 2.88 years; log-rank test, P<0.05). Functional analysis demonstrated that these signature genes were related to the activity of DNA-binding transcription activator, RNA polymerase II distal enhancer sequence-specific DNA binding, and enhancer sequence-specific DNA binding. Conclusions The results of this study showed that the signature is useful for predicting the survival of HCC patients and thus, can facilitate treatment-related decision-making.
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Affiliation(s)
- Renhua Zhang
- Information Communication Division, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Yafei Li
- Information Communication Division, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Hao Yu
- Information Communication Division, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Lin Liu
- Information Communication Division, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Changhao Zhu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Shi Zuo
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Zili Chen
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
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34
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Pogliaghi G. Liquid biopsy in thyroid cancer: from circulating biomarkers to a new prospective of tumor monitoring and therapy. Minerva Endocrinol (Torino) 2020; 46:45-61. [PMID: 33213118 DOI: 10.23736/s2724-6507.20.03339-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recently, liquid biopsy has attracted much interest as a tool for early cancer screening, prognosis, monitoring and response to treatment in many different cancer types. Indeed, liquid biopsies can be repeatedly performed in a noninvasive way, at lower cost and without the risks associated to the classic tissue biopsy. The objective of this monography was to describe the main components studied in liquid biopsy (circulating tumor nucleic acids, circulating tumor cells and extracellular vesicles) and how they have been explored in thyroid cancer, through an in-depth scientific literature review. While circulating tumor cells are the most represented component in the literature of liquid biopsy in thyroid cancer, circulating tumor nucleic acids and extracellular vesicles have also been recently explored. One important challenge in this field of research, especially for differentiated thyroid cancer, has been the low quantity of circulating components with respect to other cancer types, requiring more advanced techniques for both isolation and analysis. Despite these limitations, liquid biopsy showed promise as an additional noninvasive tool for diagnosis, prognosis, to predict outcome and therapeutic response in differentiated, medullary and anaplastic thyroid cancer.
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Affiliation(s)
- Gabriele Pogliaghi
- Division of Endocrine and Metabolic Research, IRCCS Istituto Auxologico Italiano, Cusano Milanino, Milan, Italy -
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35
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Zhang X, Zheng Y, Li G, Yu C, Ji T, Miao S. Identifying four DNA methylation gene sites signature for predicting prognosis of osteosarcoma. Transl Cancer Res 2020; 9:7299-7309. [PMID: 35117331 PMCID: PMC8798623 DOI: 10.21037/tcr-20-3204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 11/18/2020] [Indexed: 01/22/2023]
Abstract
BACKGROUND Osteosarcoma (OS) is a common malignant bone tumor in children and adolescents. DNA methylation plays a crucial role in the prognosis prediction of cancer. Identification of novel DNA methylation sites biomarkers could be beneficial for the prognosis of OS patients. In this study, we aim to find an efficient methylated site model for predicting survival in OS. METHODS DNA methylation data were downloaded from the Cancer Genome Atlas database (TCGA) and the GEO database. Cox proportional hazard regression and random survival forest algorithm (RSFVH) were applied to identify DNA methylated site signature in the samples randomly assigned to the training subset and the other samples as the test subset. By randomizing 71 clinical samples into two individual groups and a series of statistical analyses between the two groups, a DNA methylation signature is verified. RESULTS This signature comprises four methylation sites (cg04533248, cg12401425, cg13997435, and cg15075357) associated with the patient training group from the univariate Cox proportional hazards regression analysis, RSFVH, and multivariate Cox regression analysis. Kaplan-Meier survival curves showed the OS patients in the high-risk group have a poor 5-year overall survival compared with the low-risk group, and this finding was identified in the test data set. A ROC analysis was performed in the current research. The results revealed that this signature was an independent predictor of patient survival by investigating the AUC of the four methylation sites signature in the training data set (AUC =0.861) and test data set, respectively (AUC =0.920). The nomogram described in the current study placed a great guiding value for predicting 1-, 2-, 3-year survival of the OS by combining age, gender, grade, and TNM stage as covariates with the RS of patients' methylation related signatures. CONCLUSIONS Our study proved that this signature might be a powerful prognostic tool for survival rate evaluation and guide tailored therapy for OS patients.
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Affiliation(s)
- Xijun Zhang
- Department of Laboratory of Jiayuguan City First People’s Hospital, Jiayuguan, China
| | - Yongjun Zheng
- The 984th Hospital of the People’s Liberation Army, Shangzhuang Township, Beijing, China
| | - Gaoshan Li
- Department of Orthopaedics, 968 Hospital of Joint Service Support Force of Chinese People’s Liberation Army, Jinzhou, China
| | - Changying Yu
- Department of Laboratory Medicine, the 965 Hospital of the PLA, Jilin, China
| | - Ting Ji
- Shenzhen Mindray Bio-Medical Electronics Co., Ltd, Shenzhen, China
| | - Shenghu Miao
- Department of Laboratory Medicine, Wuwei People’s Hospital, Wuwei, China
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36
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Castellano GM, Pine SR. Liquid biopsies in non-small cell lung cancer management: what can we learn from methylation status and mutant allele frequencies? Transl Lung Cancer Res 2020; 9:951-955. [PMID: 32953473 PMCID: PMC7481585 DOI: 10.21037/tlcr.2020.04.05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Gina M Castellano
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.,Rutgers Graduate Program in Cellular and Molecular Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Sharon R Pine
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.,Rutgers Graduate Program in Cellular and Molecular Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.,Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.,Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
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37
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Wang R, Zhao A, Cao N, Li Z, Zhang G, Liu F. The value of circulation tumor DNA in predicting postoperative recurrence of colorectal cancer: a meta-analysis. Int J Colorectal Dis 2020; 35:1463-1475. [PMID: 32572601 DOI: 10.1007/s00384-020-03667-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/10/2020] [Indexed: 02/04/2023]
Abstract
PURPOSE Surgical resection is the primary treatment for patients with nonmetastatic colorectal cancer (CRC). However, even after undergoing radical resection procedure, 30-50% of patients will still experience relapse. Circulation tumor DNA (ctDNA), deriving from tumor cells, is shed into the bloodstream and is a potential predictive biomarker of recurrence in CRC. This meta-analysis was performed to identify the clinical value of ctDNA in predicting the recurrence of CRC patients in post-operative. METHODS PubMed, Embase, The Cochrane Library, and Web of Science were comprehensively searched to identify the studies that reported the function of ctDNA for predicting recurrence in CRC patients. The eligible studies were pooled to calculate the relative risk (RR) of recurrence in ctDNA positive and negative groups. The data of ctDNA on recurrence-free survival (RFS) were extracted and computed in hazard ratio (HR) and 95% confident interval (CI). Subgroup analyses were also performed. RESULTS A total of 7 studies including 424 patients were included and analyzed in our meta-analysis. The results showed that pooled RR was 4.65 (95%CI: 2.68-8.08, P < 0.05), indicating ctDNA positive could predict the recurrence of CRC after curative surgical. The pooled HR demonstrated strong connection between ctDNA positive and RFS in patients with CRC (HR = 9.14, 95%CI: 4.02-20.75, P < 0.05). CONCLUSION Evidence from the meta-analysis suggested that ctDNA is a promising potential biomarker for predicting postoperative recurrence of CRC. Given the inherent limitations of this study, we look forward to more well-designed clinical studies to validate and update this analysis in the future.
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Affiliation(s)
- Rui Wang
- LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Aiguang Zhao
- LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China.
| | - Nida Cao
- LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Zhaoyan Li
- LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Guangtao Zhang
- LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Feng Liu
- LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
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38
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Liu K, Tong H, Li T, Chen Y, Mao X. Potential value of circulating tumor DNA in gynecological tumors. Am J Transl Res 2020; 12:3225-3233. [PMID: 32774696 PMCID: PMC7407692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
Though the survival of patients with gynecological tumors has been significantly prolonged by radiotherapy, chemotherapy, targeted therapy and other treatments, the way to improve the patients' life quality still needs investigation. Circulating tumor DNA (ctDNA), which contains tumor genetic information, has the potential in early diagnosis of malignancies due to its high consistency with tumor tissues. Using the key words including "digital PCR", "ctDNA", "technology of digital PCR", and "detection method", "gynecological tumor", we retrieved the original articles and reviews in PubMed and WEB OF SCI database published before May 10, 2019 and performed a thorough review of them. The analysis of ctDNA could provide a comprehensive description of tumor genome, overcome the heterogeneity of tissue biopsy, and supplement the missing mutations in tissue samples. Furthermore, ctDNA could be used as a target of liquid biopsy. Our study also showed that digital PCR technology has a good potential to detect ctDNA in gynecological tumors.
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Affiliation(s)
- Kangsheng Liu
- Department of Clinical Laboratory, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjing 210029, Jiangsu, China
| | - Hua Tong
- Department of Obstetrics and Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjing 210029, Jiangsu, China
| | - Taiping Li
- Department of Neuro-Psychiatric Institute, The Affiliated Brain Hospital of Nanjing Medical UniversityNanjing 210029, Jiangsu, China
| | - Yajun Chen
- Department of Clinical Laboratory, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjing 210029, Jiangsu, China
| | - Xiaodong Mao
- Department of Endocrinology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese MedicineNanjing 210028, Jiangsu, China
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39
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Liao H, Li H. Advances in the Detection Technologies and Clinical Applications of Circulating Tumor DNA in Metastatic Breast Cancer. Cancer Manag Res 2020; 12:3547-3560. [PMID: 32547192 PMCID: PMC7244344 DOI: 10.2147/cmar.s249041] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/16/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BC) represents the most commonly diagnosed cancer among females worldwide. Although targeted therapy has greatly improved the efficacy of treating BC, a large proportion of BC patients eventually develop recurrence or metastasis. Traditional invasive tumor tissue biopsy is short of comprehensiveness in tumor assessment due to heterogeneity. Liquid biopsy, an attractive non-invasive approach mainly including circulating tumor cell and circulating tumor DNA (ctDNA), has been widely utilized in a variety of cancers with the advances of sequencing technologies in recent years. The ctDNA that is found circulating in body fluids refers to DNA released from tumor cells and has shown clinical utility in metastatic breast cancer (MBC). With the results of genomic variants detection, ctDNA could be used to predict clinical outcomes, monitor disease progression, and guide treatment for patients with MBC. Moreover, the drug resistance problem may be addressed by ctDNA detection. In this review, we summarized the technological developments and clinical applications of ctDNA in MBC.
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Affiliation(s)
- Hao Liao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, People's Republic of China
| | - Huiping Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, People's Republic of China
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40
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Stastny I, Zubor P, Kajo K, Kubatka P, Golubnitschaja O, Dankova Z. Aberrantly Methylated cfDNA in Body Fluids as a Promising Diagnostic Tool for Early Detection of Breast Cancer. Clin Breast Cancer 2020; 20:e711-e722. [PMID: 32792225 DOI: 10.1016/j.clbc.2020.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/29/2020] [Accepted: 05/11/2020] [Indexed: 12/24/2022]
Abstract
Breast malignancies are the leading type of cancer among women. Its prevention and early detection, particularly in young women, remains challenging. To this end, cell-free DNA (cfDNA) detected in body fluids demonstrates great potential for early detection of tissue transformation and altered molecular setup, such as epigenetic profiles. Aberrantly methylated cfDNA in body fluids could therefore serve as a potential diagnostic and prognostic tool in breast cancer management. Abnormal methylation may lead to both an activation of oncogenes via hypomethylation and an inactivation of tumor suppressor genes by hypermethylation. We update the state of the art in the area of aberrant cfDNA methylation analyses as a diagnostic and prognostic tool in breast cancer, report on the main technological challenges, and provide an outlook for advancing the overall management of breast malignancies based on cfDNA as a target for diagnosis and tailored therapies.
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Affiliation(s)
- Igor Stastny
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Obstetrics and Gynaecology, Martin University Hospital and Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic.
| | - Pavol Zubor
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Gynecologic Oncology, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
| | - Karol Kajo
- Department of Pathology, St Elizabeth Cancer Institute Hospital, Bratislava, Slovak Republic; Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Peter Kubatka
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic
| | - Olga Golubnitschaja
- Radiological Hospital, Rheinische, Excellence University of Bonn, Bonn, Germany; Breast Cancer Research Centre, Rheinische, Excellence University of Bonn, Bonn, Germany; Centre for Integrated Oncology, Cologne-Bonn, Excellence University of Bonn, Bonn, Germany
| | - Zuzana Dankova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic
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Alves MC, Fonseca FLA, Yamada AMTD, Barros LADR, Lopes A, Silva LCFF, Luz AS, Melo Cruz FJS, Del Giglio A. Increased circulating tumor DNA as a noninvasive biomarker of early treatment response in patients with metastatic ovarian carcinoma: A pilot study. Tumour Biol 2020; 42:1010428320919198. [PMID: 32364828 DOI: 10.1177/1010428320919198] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Detection of circulating tumor DNA is a new noninvasive technique with potential roles in diagnostic, follow-up, and prognostic evaluation of patients with many types of solid tumors. We aimed to evaluate the role of circulating tumor DNA in the setting of metastatic ovarian carcinoma. A prospective cohort of patients with metastatic ovarian cancer who were referred to systemic therapy was enrolled. Blood samples were collected before the start of treatment and monthly thereafter for 6 months. Circulating tumor DNA was quantified by real-time quantitative reverse transcription polymerase chain reaction of different lengths of Arthrobacter luteus elements as described by Umetani et al. A total of 11 patients were included, 2 for primary disease and 9 for recurrent disease. After the first cycle of chemotherapy, patients whose circulating tumor DNA levels increased from baseline were more likely to respond to chemotherapy than those whose circulating tumor DNA levels did not increase (p = 0.035). Furthermore, patients whose circulating tumor DNA levels rose after the first cycle of chemotherapy also had improved disease-free survival compared to those whose circulating tumor DNA levels did not increase (p = 0.0074). We conclude that the increase in circulating tumor DNA values collected in peripheral blood after the first cycle of systemic treatment in patients with advanced ovarian cancer is associated with an early response to systemic treatment and correlates with superior disease-free survival in this population. Circulating tumor DNA might be a specific, noninvasive, and cost-effective new biomarker of early response to systemic treatment in these patients.
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Affiliation(s)
| | - Fernando Luiz Affonso Fonseca
- Clinical Analysis Laboratory and Clinical Analysis Discipline of the ABC Foundation School of Medicine, Santo André, Brazil
| | | | | | - André Lopes
- Department of Gynecologic Oncology, Brazilian Institute for Cancer Control, São Paulo, Brazil
| | | | | | - Felipe José Silva Melo Cruz
- Department of Oncology, Brazilian Institute for Cancer Control, São Paulo, Brazil.,ABC Foundation School of Medicine, São Paulo, Brazil
| | - Auro Del Giglio
- Discipline of Hematology and Oncology at ABC Foundation School of Medicine, Brazilian Institute for Cancer Control and Hospital do Coração, São Paulo, Brazil
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42
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de Vos L, Jung M, Koerber RM, Bawden EG, Holderried TAW, Dietrich J, Bootz F, Brossart P, Kristiansen G, Dietrich D. Treatment Response Monitoring in Patients with Advanced Malignancies Using Cell-Free SHOX2 and SEPT9 DNA Methylation in Blood: An Observational Prospective Study. J Mol Diagn 2020; 22:920-933. [PMID: 32361006 DOI: 10.1016/j.jmoldx.2020.04.205] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 11/14/2019] [Accepted: 04/04/2020] [Indexed: 12/30/2022] Open
Abstract
Patients with incurable cancer usually receive palliative treatment with significant toxicity and limited efficacy. Methylation analysis of circulating cell-free DNA (ccfDNA) in blood from cancer patients represents a promising approach for minimally invasive, real-time monitoring of treatment response. Short stature homeobox 2 (SHOX2) and septin 9 (SEPT9) methylation was analyzed in N = 8865 malignant and N = 746 normal adjacent tissues across 33 different malignancies from The Cancer Genome Atlas. Furthermore, we performed quantitative SHOX2 and SEPT9 ccfDNA methylation analysis in plasma obtained before and consecutively during treatment from prospectively enrolled N = 115 patients with various advanced cancers. SHOX2 and/or SEPT9 hypermethylation in malignant tissues is present in various carcinomas, sarcoma, melanoma, brain tumors, mesothelioma, and hematopoietic malignancies. Among the prospectively enrolled cancer patients, 61% (70/115) of patients had a baseline-positive blood cumulative ccfDNA methylation score (CMS) and were eligible for response monitoring. Dynamic changes of CMS during treatment were strongly associated with treatment response. A CMS increase indicated response up to 80 days before conventional monitoring. SHOX2 and SEPT9 ccfDNA methylation represents a pan-cancer biomarker and has the potential to be a powerful tool for monitoring treatment response in patients with solid tumors and lymphomas. The early identification of nonresponders might allow for a timely change of treatment regimen.
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Affiliation(s)
- Luka de Vos
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Maria Jung
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Ruth-Miriam Koerber
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Emma G Bawden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Tobias A W Holderried
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Jörn Dietrich
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Friedrich Bootz
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Peter Brossart
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | | | - Dimo Dietrich
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany.
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43
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Caruso C, Garofalo C. Pharmacogenomics Biomarkers of Soft Tissue Sarcoma Therapies. Front Oncol 2020; 10:509. [PMID: 32351891 PMCID: PMC7174622 DOI: 10.3389/fonc.2020.00509] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 03/20/2020] [Indexed: 12/19/2022] Open
Abstract
Soft tissue sarcomas (STS) are heterogeneous rare malignancies comprising ~1% of all solid cancers in adults and including more than 70 histological and molecular subtypes with different pathological and clinical development characteristics. Over the last two decades, the increased knowledge of the new molecular and genomic mechanisms of different STS histotypes allowed for a reclassification of these tumors and consequently to the development of novel chemotherapeutic agents. Generally, surgery, in combination with radiotherapy only in selected cases of localized disease, represents the most common treatment of primary STS, whereas the principal treatment modality for locally advanced or metastatic disease is first-line chemotherapy. The principal treatment for the preponderance of STS patients is usually an anthracycline (epirubicin and doxorubicin) in monotherapy or in combination with other drug novel chemotherapeutic agents. However, survival for treated patients with metastatic disease is poor, and a 2-years survival rate is about 30%. In this scenario, Pharmacogenomics (PGx) biomarkers that can predict drug response play an important role in the improvement of molecular diagnostics in clinical routines and contribute to elucidating the genetic basis for the differences in treatment efficacy and toxicity among STS patients. This review focuses on recent insight in the PGx biomarkers that have been described to modulate responsiveness and toxicity parameters of conventional and new chemotherapeutics drugs in several STS histotypes.
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Affiliation(s)
| | - Cecilia Garofalo
- Advanced Translational Research Laboratory, Veneto Institute of Oncology IOV – IRCCS, Padua, Italy
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44
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Zhang S, Su M, Sun Z, Lu H, Zhang Y. The signature of pharmaceutical sensitivity based on ctDNA mutation in eleven cancers. Exp Biol Med (Maywood) 2020; 245:720-732. [PMID: 32050795 DOI: 10.1177/1535370220906518] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
IMPACT STATEMENT Gene mutations are closely related to cancers and drug sensitivity and noninvasive liquid biopsy was used to detect mutations of ctDNA in plasma. In this study, we performed exon sequencing of 416 cancer-related genes for cancer primary tissue and plasma samples of 20 patients in 11 cancers and obtained the comprehensive mutation landscape. We found that liquid biopsy is reliable in place of tissue biopsy. And 31 potential unique mutation prognostic markers were screened in 7 cancer types. Moreover, the drug-mutation network (DMN) was constructed and 9 gene mutations (B-Mut-9) were confirmed that can be served as drug biomarkers in blood. Our study showed that the variation in ctDNA can be used as the biomarkers for cancer prognosis and drug efficacy prediction. This can provide a reference for clinical noninvasive testing.
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Affiliation(s)
- Shumei Zhang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin 150040, China
| | - Mu Su
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Zhongyi Sun
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Haibo Lu
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Yan Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 51000, China
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45
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Colao A, de Nigris F, Modica R, Napoli C. Clinical Epigenetics of Neuroendocrine Tumors: The Road Ahead. Front Endocrinol (Lausanne) 2020; 11:604341. [PMID: 33384663 PMCID: PMC7770585 DOI: 10.3389/fendo.2020.604341] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/12/2020] [Indexed: 12/16/2022] Open
Abstract
Neuroendocrine tumors, or NETs, are cancer originating in neuroendocrine cells. They are mostly found in the gastrointestinal tract or lungs. Functional NETs are characterized by signs and symptoms caused by the oversecretion of hormones and other substances, but most NETs are non-functioning and diagnosis in advanced stages is common. Thus, novel diagnostic and therapeutic strategies are warranted. Epigenetics may contribute to refining the diagnosis, as well as to identify targeted therapy interfering with epigenetic-sensitive pathways. The goal of this review was to discuss the recent advancement in the epigenetic characterization of NETs highlighting their role in clinical findings.
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Affiliation(s)
- Annamaria Colao
- Department of Clinical Medicine and Surgery, Unesco Chair Health Education and Sustainable Development, Federico II University of Naples, Naples, Italy
| | - Filomena de Nigris
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Roberta Modica
- Department of Clinical Medicine and Surgery, Federico II University of Naples, Naples, Italy
- *Correspondence: Roberta Modica,
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
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46
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He K, Zhang S, Shao LL, Yin JC, Wu X, Shao YW, Yuan S, Yu J. Developing more sensitive genomic approaches to detect radioresponse in precision radiation oncology: From tissue DNA analysis to circulating tumor DNA. Cancer Lett 2019; 472:108-118. [PMID: 31837443 DOI: 10.1016/j.canlet.2019.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/02/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023]
Abstract
Despite the common application and considerable efforts to achieve precision radiotherapy (RT) in several types of cancer, RT has not yet entered the era of precision medicine; the ability to predict radiosensitivity and treatment responses in tumors and normal tissues is lacking. Therefore, development of genome-based methods for individual prognosis in radiation oncology is urgently required. Traditional DNA sequencing requires tissue samples collected during invasive operations; therefore, repeated tests are nearly impossible. Intra- and inter-tumoral heterogeneity may undermine the predictive power of a single assay from tumor samples. In contrast, analysis of circulating tumor DNA (ctDNA) allows for non-invasive and near real-time sampling of tumors. By investigating the genetic composition of tumors and monitoring dynamic changes during treatment, ctDNA analysis may potentially be clinically valuable in prediction of treatment responses prior to RT, surveillance of responses during RT, and evaluation of residual disease following RT. As a biomarker for RT response, ctDNA profiling may guide personalized treatments. In this review, we will discuss approaches of tissue DNA sequencing and ctDNA detection and summarize their clinical applications in both traditional RT and in combination with immunotherapy.
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Affiliation(s)
- Kewen He
- Department of Radiology, Shandong Cancer Hospital affiliated to Shandong University, Jinan, Shandong, 250117, People's Republic of China; Department of Radiology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, People's Republic of China
| | - Shaotong Zhang
- Department of Cardiology, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong, 250013, People's Republic of China
| | - Liang L Shao
- Geneseeq Technology Inc., Toronto, Ontario, M5G 1L7, Canada
| | - Jiani C Yin
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, 210032, People's Republic of China
| | - Xue Wu
- Geneseeq Technology Inc., Toronto, Ontario, M5G 1L7, Canada
| | - Yang W Shao
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, 210032, People's Republic of China; School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 210029, People's Republic of China
| | - Shuanghu Yuan
- Department of Radiology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, People's Republic of China.
| | - Jinming Yu
- Department of Radiology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, People's Republic of China.
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47
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Mauger F, Tost J. Enhanced- ice-COLD-PCR for the Sensitive Detection of Rare DNA Methylation Patterns in Liquid Biopsies. Bio Protoc 2019; 9:e3452. [PMID: 33654946 DOI: 10.21769/bioprotoc.3452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 11/18/2019] [Accepted: 11/18/2019] [Indexed: 11/02/2022] Open
Abstract
In the context of precision medicine, the identification of novel biomarkers for the diagnosis of disease, prognosis, predicting treatment outcome and monitoring of treatment success is of great importance. The analysis of methylated circulating-cell free DNA provides great promise to complement or replace genetic markers for these applications, but is associated with substantial challenges. This is particularly true for the detection of rare methylated DNA molecules in a limited amount of sample such as tumor released hypermethylated molecules in the background of DNA fragments from normal cells, especially lymphocytes. Technologies for the sensitive detection of DNA methylation have been developed to enrich specifically methylated DNA or unmethylated DNA using among other methods: enzymatic digestion, methylation-specific PCR (often combined with TaqMan like oligonucleotide probes (MethyLight)) and co-amplification at lower denaturation temperature PCR (COLD-PCR). E-ice-COLD-PCR (Enhanced-improved and complete enrichment-COLD-PCR) is a sensitive method that takes advantage of a Locked Nucleic Acid (LNA)-containing oligonucleotide probe to block specifically unmethylated CpG sites allowing the strong enrichment of low-abundant methylated CpG sites from a limited quantity of input. E-ice-COLD-PCRs are performed on bisulfite-converted DNA followed by Pyrosequencing analysis. The quantification of the initially present DNA methylation level is obtained using calibration curves of methylated and unmethylated DNA. The E-ice-COLD-PCR reactions can be multiplexed, allowing the analysis and quantification of the DNA methylation level of several target genes. In contrast to the above-mentioned assays, E-ice-COLD-PCR will also perform in the presence of frequently occurring heterogeneous DNA methylation patterns at the target sites. The presented protocol describes the development of an E-ice-COLD-PCR assay including assay design, optimization of E-ice-COLD-PCR conditions including annealing temperature, critical temperature and concentration of LNA blocker probe followed by Pyrosequencing analysis.
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Affiliation(s)
- Florence Mauger
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
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48
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Xia S, Ye J, Chen Y, Lizaso A, Huang L, Shi L, Su J, Han-Zhang H, Chuai S, Li L, Chen Y. Parallel serial assessment of somatic mutation and methylation profile from circulating tumor DNA predicts treatment response and impending disease progression in osimertinib-treated lung adenocarcinoma patients. Transl Lung Cancer Res 2019; 8:1016-1028. [PMID: 32010579 DOI: 10.21037/tlcr.2019.12.09] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background Circulating tumor DNA (ctDNA) harboring tumor-specific genetic and epigenetic aberrations allows for early detection and real-time monitoring of tumor dynamics. In this study, we aimed to evaluate the potential of parallel serial assessment of somatic mutation and methylation profile in monitoring the response to osimertinib of epidermal growth factor receptor (EGFR) T790M-positive advanced lung adenocarcinoma patients. Methods Parallel somatic mutation and DNA methylation profiling was performed on a total of 85 longitudinal plasma samples obtained from 8 stage IV osimertinib-treated EGFR T790M-positive lung adenocarcinoma patients. Results Our results revealed a significant correlation between the by-patient methylation level with the maximum allele fraction (maxAF, P=0.0002). The methylation levels were significantly higher in the plasma samples of patients with detectable somatic mutations than patients without somatic mutations (P=0.0003) and healthy controls (P=0.0018). Moreover, analysis of both the DNA methylation level and maxAF revealed four trends of treatment response. Collectively, the decrease in methylation level and maxAF reflected treatment efficacy, while the gradual increase reflected impending disease progression (PD). Elevated methylation levels and maxAF were observed in 6 and 5 patients in an average lead-time of 3.0 and 1.9 months, respectively, prior to evaluation of PD using radiological imaging. Conclusions DNA methylation profiling has the potential to predict disease relapse prior to evaluation through radiological modalities, suggesting that serial assessment of methylation level in combination with somatic mutation profiling are reliable methods for treatment monitoring. These methods should thus be incorporated with imaging modalities for a more comprehensive work-up of treatment response, particularly for patients treated with targeted therapies.
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Affiliation(s)
- Shu Xia
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Affiliated Hospital of Qinghai University, Xining 810000, China
| | - Junyi Ye
- Burning Rock Biotech, Guangzhou 510300, China
| | - Yu Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | | | - Le Huang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Lei Shi
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jing Su
- Burning Rock Biotech, Guangzhou 510300, China
| | | | | | - Lingling Li
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuan Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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49
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Kerachian MA, Poudineh A, Thiery JP. Cell free circulating tumor nucleic acids, a revolution in personalized cancer medicine. Crit Rev Oncol Hematol 2019; 144:102827. [DOI: 10.1016/j.critrevonc.2019.102827] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/13/2019] [Accepted: 10/22/2019] [Indexed: 02/07/2023] Open
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50
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Abstract
Breast cancer is a highly heterogeneous and dynamic disease, exhibiting unique somatic alterations that lead to disease recurrence and resistance. Tumor biopsy and conventional imaging approaches are not able to provide sufficient information regarding the early detection of recurrence and real time monitoring through tracking sensitive or resistance mechanisms to treatment. Circulating tumor DNA (ctDNA) analysis has emerged as an attractive noninvasive methodology to detect cancer-specific genetic aberrations in plasma including DNA mutations and DNA methylation patterns. Numerous studies have reported on the potential of ctDNA analysis in the management of early and advanced stages of breast cancer. Advances in high-throughput technologies, especially next generation sequencing and PCR-based assays, were highly important for the successful application of ctDNA analysis. However, before being integrated into clinical practice, ctDNA analysis needs to be standardized and validated through the performance of multicenter prospective and well-designed clinical studies. This review is focused on the clinical utility of ctDNA analysis, especially at the DNA mutation and methylation level, in breast cancer patients, incorporating the latest advances in technological approaches and involving key studies in the early and metastatic setting.
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Affiliation(s)
- Eleni Tzanikou
- Department of Chemistry, Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, University of Athens, Athens, Greece
| | - Evi Lianidou
- Department of Chemistry, Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, University of Athens, Athens, Greece
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